However, during transport, something happens to their patterns. The transporter chief cannot get them to rematerialize, so she aborts. However, they do not rematerialize at the original coordinates as the safety protocols indicated. Riker and the engineer conclude they are gone.

The Romulans are still looking at a core breach. Lt. Commander Data and two more engineers go to the ship in a shuttle. When the pressure in the core jumps up, Riker, Worf, and the Romulans are forced to eject it manually, and do so just in time.

The Enterprise begins to transfer power to the Romulan ship, as Data examines the transporters for anything that could cause the safety systems to fail. He finds an energy fluctuation and begins investigating it. He also asks if he may arrange the memorial service, and Captain Picard grants his request.

La Forge also soon finds that he has the same problems as Ro. When she finds him, they start speculating about what happened. La Forge and Ro take two different approaches to their apparent death. Ro tries to accept her death and be at peace with herself. La Forge is determined to figure out what happened, convinced they are still alive.

While the chief engineer begins to follow Data's investigation, Ro wanders around the ship, and finds herself in the captain's ready room when Commander Riker tells Picard that he wants to say a few words about her. This surprises and upsets her, given that she doesn't think he knows her that well. She also begins to speak her mind to the captain and others who can't hear her, telling Picard that she was glad he trusted her. After that, La Forge enters and talks her into going over to the Romulan vessel, where Data believes the problem originated. They take his shuttle, and overhear Data talking to Worf about the memorial service (to which Ro responds with a groan, "Please, not the death chant.")

Using his ability to look through the casing, La Forge discovers that a central device in the Romulan engine room is a phase inverter, which can transform normal matter so it will pass through other matter and energy. He realizes this explains the chroniton fields, and the pair's abilities; they are alive, just "out of phase" with normal matter and energy.

After Data is called away, the two of them then hear a Romulan plot to destroy the Enterprise so they don't find out about the technology, and when they return to the ship, a phased Romulan follows them.

When Data and the transporter chief scan for chroniton fields, using anyons to eliminate them, La Forge realizes that he and Ro are leaving chroniton particles behind them. La Forge tries to get Data to recognize the pattern of his movements, and accidentally finds the solution to his problem; a "careless" sweep from Data hits Geordi on the hand, stinging him – and after discovering that this hand no longer went right through the master systems display table as easily, he realizes that the anyons partially re-phased his hand. He doubles his efforts, desperately hoping to make Data turn up the intensity so he will be brought back, but to no avail. Data gives up.

Unfortunately, when Ro is following the transporter chief, the Romulan confronts her with a "phased" disruptor. He forces Ro to take him to La Forge, but on the other side of a wall, she jumps him, and knocks him down. A chase ensues, and Ro gets shot in the leg with the disruptor. A fist fight ensues, and La Forge enters (following Data to a very large chroniton field created by the weapon's fire) and knocks the Romulan through the ship's hull, and out into space, an action that saves Ro's life.

Afterward, the power transfer beam is disconnected, Picard is thanked, and they are about to engage at warp, when the transporter chief reminds him the decontamination is still going on, and they shouldn't use any major system until it has been completed. La Forge figures that for them to be returned to normal, they will have to be hit with a very large anyon field, and since it will only work for a millisecond, someone will need to be looking right at them. When the memorial service in Ten Forward is announced, they go there. Joining Picard and Riker in the turbolift, La Forge hears the captain, practicing his eulogy, recall their first meeting years before, while Ro anxiously wonders what Riker will say about her – but they reach Ten Forward first, leaving her even more frustrated. To Ro's shock and La Forge's pleasant surprise, the atmosphere in Ten Forward is rather festive (complete with a jazz band, which Riker eventually joins) as everyone mingles and reminisces.

They start shooting everything with the disruptor – approaching Riker, Ro sarcastically notes that she would never know what he was to say about her before putting a shot through his head. Soon, the chief finds the very large field forming in Ten Forward. However, their attempts to get attention when the field strength is increased fail, and the Enterprise will need to get to Garadius IV soon. So, they make the disruptor overload, and sure enough, a much larger decontamination is attempted. This time, they are seen by Data and the Captain. As Picard wonders what they have just seen, only now does Data put their appearances together with all of the chroniton phenomena – they had been "cloaked" in some manner, and the anyons "de-cloaked" them. When the anyon field is put on its highest setting, all of the particles are purged, and the mourners look on in disbelief as the "dearly departed" reappear at their own memorial. Right away, La Forge gives the order to take the warp engines offline – when the ensign in charge at engineering, understandably suspicious of a command from his dead superior, contacts Picard, the captain assures him that he heard right, and the order was valid – and the muon wave is removed before they get underway. With that crisis averted, Geordi calls on the party to continue, which does with a much more joyous atmosphere.

Afterward, with the pair eating after the party has concluded, Ro notes that she gained a new appreciation for her culture's religious beliefs that she once dismissed. At this confession, La Forge playfully suggests they should develop their own interphase device since if it can teach Ensign Ro humility, then it is surely capable of anything.

"But my uniform - my VISOR – are you saying I'm some blindghost with clothes!?"
"I don't have all the answers! I've never been dead before!"

- La Forge and Ro

"I might like to say a few words..."
"You did know La Forge longer than any of us."
"Actually, I was thinking more about Ensign Ro."

- Riker and Picard

"Me?!?!...Wait a minute, what're you gonna say about me?!"

- Ro, overhearing Riker

"I just... wanted to say thank you...for trusting in me when no one else would."

- Ro, believing she's dead, saying "goodbye" to Picard

"Why can't you just accept the fact..."
"Look - if you're right, then we're dead, and this doesn't make any difference. But if I'm right, then we're still alive - and I'm gonna need your help!"

- Ro and La Forge

"I never knew what a friend was, until I met Geordi. He spoke to me as though I were Human. He treated me no differently from anyone else. He accepted me for what I am. And that - I have learned - is friendship."

- Data to Worf, about La Forge - who heard the whole thing

"Data, that's a nice sentiment - but a little premature."

- La Forge, in response to Data's speech

"I'm dead!"

- Ro

"I've been thinking about the first time I met Geordi La Forge. He was a young officer, assigned to pilot me on an inspection tour, and... I made some off-hand remark about the... the shuttle's engine efficiency not being what it should, and the next morning I found that... he'd stayed up all night, re-fitting the fusion initiators. Well, I knew then that I wanted to have him with me on my next command."

- Picard, practicing a eulogy he wouldn't have to give

"Have you decided what you're going to say about Ensign Ro?"
"Yes I have. It wasn't easy..."

- Picard and Riker, arriving at Ten Forward

"What... What wasn't easy?!...WHAT?!?!?!"

- Ro, once again hearing not quite enough from Riker

"Well, this is... unusual."
(grinning widely) "Yeah. I think I like it!"

- Picard and Riker at La Forge and Ro's highly festive funeral.

"Now I suppose I'll never know what you were gonna say about me!"

- Ro, to Riker who can't hear her, before "shooting" him in the head with a phased (and therefore harmless) disruptor

"C'mon, Data - put it all together now!!!"

- La Forge, having been seen by Data and Picard

"These were not ghosts - what did we see?"
"I believe I may know what has happened, sir..."
"Oh, Data, PLEASE be right!"
"...it would explain the mysterious chroniton fields...if they were cloaked in some way!"
"You're saying that they're still alive?!"
"If I am right, sir, they are - and in this room. Their brief appearance coincided with the anyon sweep - perhaps the anyons neutralize the cloaking effect."

- Picard, and Data (with a little encouragement from La Forge), figuring out what happened

"Data, do you see us?"
"Of course."

- La Forge, back in phase and Data

"Take the warp engines off-line until further notice...there's a muon wave building up in the dilithium chamber."
"Captain... who gave that order?!"
"That was Commander Geordi La Forge, Ensign - please follow his instructions."

- La Forge (aware of the Romulan sabotage), Engineering Ensign (suspicious of an order from his "dead" superior), and Picard (assuring him that it was in fact Geordi)

"Looks like a great party - mind if we join you?"

- La Forge, having re-appeared at his own funeral

"Thanks, Data. I've never been to a better funeral."

- La Forge

"We should develop our own interphase device. If it can teach Ro Laren humility, it can do anything."

According to Michael Piller, "I get a little tired of Romulans and I was a little reluctant to make this a Romulan show...It had been pitched as actually similar stories by two people. We brought the ideas and combined them into one and Ron developed the story and wrote it. I think it's terribly important to give credit to Ron Moore for the work he did this season." (Captains' Logs: The Unauthorized Complete Trek Voyages)

According to Brannon Braga, the story originally involved Troi rather than Ro. He noted, "Troi's had enough running and jumping this year. We felt why not give Ro something and I'm glad she did, because she kicks a Romulan in the chest and does a kick worthy of Bruce Lee. She's some sort of acrobat. That scene in my opinion makes the whole show." (Captains' Logs: The Unauthorized Complete Trek Voyages)

Director David Carson recalled, "This was an extremely difficult episode to do, because it dealt with special effects of a type people were familiar with from Ghost, which Star Trek had never attempted before. It was one of the most difficult technical episodes they'd ever done just by the nature of having people walk through people and an environment where people exist in different phases. I thought the story hung together quite well, and it turned out in quite a good way." (Captains' Logs: The Unauthorized Complete Trek Voyages)

Rick Berman remarked, "I hate that title, but I'm very pleased with the episode. It's a wonderful high concept story. The story really pumps along and there's great Romulan mystique and some wonderful things with people running through walls and the audience gets to see two different realities...It's a great piece of science fiction." (Captains' Logs: The Unauthorized Complete Trek Voyages)